When a mosquito alights on the skin, it attempts to pierce a small blood vessel with its proboscis in order to suck blood. To prevent the blood from coagulating, the mosquito first injects some saliva. As well as vasodilating agents this saliva also contains anticoagulantia and enzymes such as apyrase which inhibit blood platelet aggregation (apyrase hydrolyses ADP, a substance which promotes the aggregation of thrombocytes). However, the saliva may also contain micro-organisms. When a human is bitten by an Anopheles infected with malaria, parasites (sporozoites) [Gr. sporos = seed, spore; zoon = animal] are introduced into the human body. These sporozoites pass into the liver within 30 minutes. A certain protein of the parasite, (the circumsporozoite protein, CSP), plays an important role in the penetration of the sporozoite into a liver cell. The parasites reproduce asexually (schizogony) in liver cells [Gr. schizo = split, divided; etymology similar to schizophrenia]. This is called exo-erythrocytic (or pre-erythrocytic) reproduction. This part of the life cycle was first described by Shortt and Garnham in 1948. The parasite grows and undergoes several nuclear divisions without the cytoplasm dividing. It reaches a diameter of 30-70 µm. The form of the parasite produced in this way is called a liver schizont. No malaria pigment is present (see below). Division of the cytoplasm then follows and the multinuclear schizont splits into many thousands of small offspring (merozoites) [Gr. meros = part; cf. polymer]. Every successful sporozoite can produce some 20,000 merozoites. These initially measure only 0.7 µm. After some time the infected liver cells burst and the merozoites enter the blood stream. While the parasites are still reproducing in the liver, there are no symptoms. Neither the sporozoites, nor the liver forms are sensitive to most of the drugs used in prophylaxis. The minimally required time from infection to the appearance of the first merozoites, is the prepatent period. The incubation period is somewhat longer because signs and symptoms do not appear until the parasitaemia is sufficiently advanced.

In the case of P. vivax and P. ovale only some of the infected liver cells burst. The parasites in the liver cells which do not burst (hypnozoites) [Gr. hypnos = sleep; cf. hypnosis] may remain for years and are responsible for new attacks of the disease if reactivated. The trigger which reactivates the hypnozoites is not known. The existence of hypnozoites in P. vivax was only demonstrated in 1985, via fluorescence microscopy. Reactication of these "sleeping" forms explains delayed exacerbations of the disease after treatment with chloroquine. Chloroquine kills the blood forms, but not the liver forms which are responsible for a renewed exacerbation later. Hypnozoites are not present in P. falciparum and probably not in P. malariae. This is important for treatment, because hypnozoites are not sensitive to chloroquine, quinine, mefloquine or artemisinin. Accidental inoculation with infected blood (blood containing trophozoites) may lead to infection, e.g. transfusion malaria or malaria via shared contaminated syringes by drug users. Since the infection in these cases is not transmitted by sporozoites, there are no liver forms. Liver forms are also absent in congenital malaria. This is important for treatment (no primaquine for congenital malaria with P. vivax or P. ovale). The chronic nature of infections with P. malariae is traditionally explained by assuming that the parasite can induce a very low parasitaemia for many years, which is below the detection threshold of normal diagnostic methods.

The merozoites carry certain proteins on their membranes (MSP-1 or merozoite surface protein-1). This MSP-1 binds to the surface of the erythrocyte. The merozoites subsequently penetrate the red blood cells. Precisely how the parasites penetrate the red blood cells without haemolysing them is not yet completely understood. They apparently use an unusual actin-myosin molecular motor (acto-Pfmyo-A). They remain in a vacuole in the erythrocyte. Some researchers think that there is a pathway between the extracellular space and the vacuole containing the intracellular parasite. This system could explain how macromolecules get into the parasite (erythrocytes have no capacity for endocytosis). This concept is, however, controversial and could possibly be due to an in-vitro artefact. The MSP-1 protein is highly variable and the parasite may change the structural details even within the course of a single infection. The parasite thus escapes the host's immunological defence mechanisms.

In the red blood cell the parasite feeds on haemoglobin. The form of the parasite is now known as a trophozoite (Gr. trophe = nutrition). The young parasite possesses a digestive vacuole with lysosomal enzymes. This vacuole contains proteinases (plasmepsin and falcipain). The vacuole can be clearly seen in a blood smear and explains the ring shape of the young parasite. The breakdown of haemoglobin results in an iron-containing pigment: haemozoin. This can be seen after 12-24 hours as malaria pigment (see below: diagnosis). The vacuole disappears as the parasite becomes older. The trophozoites will once more reproduce asexually and lead to the formation of a multinuclear parasite (schizont). The latter divides to form merozoites. Each schizont produces 8 to 24 merozoites, depending on the species, within a time span of 48 hours (P. falciparum, P. vivax, P. ovale) or 72 hours (P. malariae). The infected red blood cells burst after a while so that once more merozoites appear in the blood from where they will penetrate into new erythrocytes within a few seconds. This bursting (lysis) of the red blood cells is accompanied by a bout of fever. If the development is synchronous (all parasites being at the same stage of development) the fever will follow a typical pattern (see below). This is, however, unusual. The development from merozoite to schizont takes place in the peripheral blood and all stages can be observed. In P. falciparum usually only very young forms (ring forms) can be observed in the peripheral blood because older parasites adhere to the endothelium of blood vessels in deep organs (e.g. the brain).

After a few days some of the merozoites transform into male or female gametocytes. These are necessary for sexual reproduction of the parasite. Generally at least two schizogonous cycles must be completed before gametocytes appear. The trigger for the production of gametocytes is not known. Gametocytes are responsible for transmitting the disease but do not themselves cause symptoms. Adult P. falciparum gametocytes are not sensitive to chloroquine and quinine, while those of P. vivax, P. ovale and P. malariae are sensitive. This means that following adequate treatment of P. falciparum there may still be gametocytes in the blood, and this may continue for several weeks. This does not mean that the treatment has failed. One interesting hypothesis is that chloroquine might significantly increase the gametocytaemia of chloroquine-resistant P. falciparum, resulting in an increased infectivity for Anopheles. This could, therefore, contribute to the rapid spread of chloroquine resistance.

If the gametocytes are ingested during a bite from an Anopheles, the male gametocyte will quickly divide mitotically 3 times and develop several flagellae (exflagellation) [L. flagellum = whip]. After ten minutes microgametes [Gr. gamos = marriage] are formed from one male gametocyte. A microgamete is approximately 20 µm long and actively motile. Exflagellation is triggered among other things by a fall in temperature and by higher pH (between 8 and 8.3). The latter, however, only applies in vitro. The acidity in the insect’s stomach is always approximately the same as that of the blood ingested. A certain substance in the insect, the gametocyte-activating factor, plays a role in the activation which makes alkalisation unnecessary. This factor is a small molecule (xanthurenic acid). This heterocyclic double ring originates from the catabolism of tryptophan and is a by-product of the synthesis of ocular pigment in the insect. The substance is present in higher concentrations in malaria vectors than in human blood. That is one of the reasons for the absence of gametocyte activation in humans.

The peak of exflagellation occurs within 25 minutes after the blood meal. The female gametocyte will undergo a slight change in shape and is then called a macrogamete. The gametes are anisogamous (they differ in size). Within 3 hours after the blood meal the microgamete and macrogamete will fuse in the mosquito’s stomach to form a diploid zygote (fertilised ovum) [Gr. "zygotos": yoked together]. Thus fertilisation occurs in the insect!

In the following 5 hours the zygote will undergo meiosis, resulting in 4 haploid parasites. During meiosis cross-over may occur between homologous chromosomes, which results in genetic recombination. Since in natural infections parasites are often of different genotypes, this is a mechanism for maintaining diversity within one species. Later the parasite will become motile. This form of the parasite is now called an ookinete (Gr. oon = egg; kinetos = movement). The blood in the mosquito’s intestine is separated from the midgut epithelium by a semi-permeable membrane (like a dialysis membrane). Because this membrane envelops the food, it is called the peritrophic membrane (Gr. peri = around; trophe = nutrition). The ookinete penetrates this chitinous membrane which lines the inner side of the mosquito’s intestine. To do this the parasite secretes a prochitinase, an enzyme which will be converted to an active form by the mosquito’s digestive enzymes (trypsins). The ookinete subsequently migrates through the mosquito’s intestinal wall, mainly via certain epithelial cells (Ross' cells) which contain fewer microvilli than other nearby intestinal cells. The ookinete does not penetrate the basal membrane which encloses the intestinal cells on the haemocoel side. All the steps described above are essential for the maturation of the parasite and the midgut is therefore an important barrier. Only a few gametocytes in the blood meal will become successfully penetrating ookinetes. Once the ookinete has penetrated the intestine, it attaches to the outer side of the intestine. There the ookinete changes into an immobile oocyst. This is initially quite small (6-8 µm). It then grows to a diameter of 40-60 µm. After approximately a week (depending on the temperature) and after repeated mitotic nuclear divisions in the oocyst, countless 10-15 µm long fusiform parasites are produced. Thousands of sporozoites are formed, which after rupture of the oocyst will migrate to the mosquito's thoracic three-lobed salivary glands. They seem to have a preference for the distal-lateral and medial lobes of the salivary glands. The sporozoites mature in the salivary glands and are then ready to be injected into a human during the insect’s next blood meal.

The trophozoite has no carbohydrate reserves and needs to consume glucose continually. The glucose metabolism in infected red blood cells is 50-100 times higher than that in non-infected cells. This probably contributes to the hypoglycaemia which is often seen in severe infections. The parasite does have mitochondria, but these play a minor role in the provision of energy (the last word on this has not yet been said). Glucose is converted by anaerobic glycolysis to pyruvate and then to lactate. This latter step, as in humans, is catalysed by the enzyme lactate dehydrogenase (LDH). The parasite’s LDH is clearly different from that of humans and forms the basis of a diagnostic test (see below). Some glucose is processed in the hexose monophosphate shunt, which serves to produce NADPH. NADPH is necessary for the protective antioxidant glutathione, for reductive biosynthesis and for the de novo production of purines (see also G6PD-deficiency). Purines are necessary to produce parasitic DNA and glutathione is needed as a protection against oxidative stress. This may explain why G6PD-deficiency should offer relative protection against malaria and why this deficiency occurs frequently in malaria regions. However, opinions are divided on this subject.

In 1999 it was shown that Plasmodium berghei uses two different kinds of ribosome, one which is active in the mosquito and one in its normal rodent host. Whether this is also the case with other parasites is as yet unclear.