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Background  Further reductions in malaria incidence as more countries approach malaria elimination require the identification and treatment of asymptomatic individuals who carry mosquito-infective  Plasmodium  gametocytes that are responsible for furthering malaria transmission. Assessing the relationship between total parasitaemia and gametocytaemia in field surveys can provide insight as to whether detection of low-density, asymptomatic  Plasmodium falciparum  infections with sensitive molecular methods can adequately detect the majority of infected individuals who are potentially capable of onward transmission.    Methods  In a cross-sectional survey of 1354 healthy children and adults in three communities in western Kenya across a gradient of malaria transmission (Ajigo, Webuye, and Kapsisywa–Kipsamoite), asymptomatic  P. falciparum  infections were screened by rapid diagnostic tests, blood smear, and quantitative PCR of dried blood spots targeting the  varATS  gene in genomic DNA. A multiplex quantitative reverse-transcriptase PCR assay targeting female and male gametocyte genes ( pfs25 ,  pfs230p ), a gene with a transcriptional pattern restricted to asexual blood stages ( piesp2 ), and human  GAPDH  was also developed to determine total parasite and gametocyte densities among parasitaemic individuals.    Results  The prevalence of  varATS -detectable asymptomatic infections was greatest in Ajigo (42%), followed by Webuye (10%). Only two infections were detected in Kapsisywa. No infections were detected in Kipsamoite. Across all communities, children aged 11–15 years account for the greatest proportion total and sub-microscopic asymptomatic infections. In younger age groups, the majority of infections were detectable by microscopy, while 68% of asymptomatically infected adults (> 21 years old) had sub-microscopic parasitaemia.  Piesp2 -derived parasite densities correlated poorly with microscopy-determined parasite densities in patent infections relative to  varATS -based detection. In general, both male and female gametocytaemia increased with increasing  varATS -derived total parasitaemia. A substantial proportion (41.7%) of individuals with potential for onward transmission had qPCR-estimated parasite densities below the limit of microscopic detection, but above the detectable limit of  varATS  qPCR.    Conclusions  This assessment of parasitaemia and gametocytaemia in three communities with different transmission intensities revealed evidence of a substantial sub-patent infectious reservoir among asymptomatic carriers of  P. falciparum . Experimental studies are needed to definitively determine whether the low-density infections in communities such as Ajigo and Webuye contribute significantly to malaria transmission.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12936-021-03905-w.

The prevalence and density of asymptomatic Plasmodium falciparum infections among children and adults in three communities of western Kenya