The paracentric inversion polymorphisms of Anopheles gambiae and An. arabiensis populations in the Kisumu area of western Kenya were studied in relation to parameters of Plasmodium falciparum transmission. Anopheles gambiae (n = 1, 387) was polymorphic for inversions b on chromosomal arm 2R and a on arm 2L, with frequencies of the inverted arrangements of 17% and 43%, respectively. Anopheles arabiensis (n = 484) was polymorphic for inversion b on chromosomal arm 2R and a on 3R, with frequencies of the inverted arrangements of 58% and 5%, respectively. Observed karyotypic frequencies did not deviate from Hardy-Weinberg equilibrium, indicating a condition of panmixia (i.e., random mating) for both species. The overall degree of intraspecific polymorphism was low, confirming findings from other zones of East Africa. No significant differences in inversion frequencies of either An. gambiae or An. arabiensis were observed, either between collecting sites or between similar sampling periods of consecutive years. At the same time, a stable, significant two-fold difference in Plasmodium infection rates was detected among An. gambiae carriers of different inversion karyotypes on chromosome 2. A significant non-uniform distribution of human- and bovid-fed specimens was also detected among the carriers of different 2Rb inversion karyotypes in indoor resting An. arabiensis. Relationships among inversion karyotypes of the two major malaria vectors in the An. gambiae complex and key factors affecting malaria transmission intensity emphasize that intraspecific variation could contribute significantly to the diversity and stability of malaria vectorial systems in Africa.