The objective of this study was to investigate the gastro-intestinal (GIT) parasites commonly occurring in captive and wild-trapped (WT) non-human primates (baboons, vervets and Sykes) in Kenya and compare their prevalence. Three hundred and fifteen faecal samples were subjected to a battery of diagnostic tests, namely, direct smear, modified formal ether sedimentation, Kato thick smear, Harada-Mori techniques for parasite detection and culture to facilitate nematode larvae identification. Of these, 203 (64.4%) harboured helminths and 54 (17.1%) had protozoa. The helminth parasites comprised Strongyloides fulleborni 141 (44.8%), Trichuris trichuira 200 (63.5,%), Oesophagostomum sp. 48 (15.2%), Trichostrongylus sp. 73 (23.2%), Enterobius vermicularis 44 (14.0%), Schistosoma mansoni 4/92 (4.3%) and Streptopharagus sp. 68 (21.6%). Protozoan parasites consisted of Entamoeba coli 204 (64.8%), Balantidium coli 127 (40.3%) and Entamoeba histolytica 78 (24.8%). Both WT and colony-borne (CB) primates had similar species of parasites, but higher prevalences of protozoan infection were observed in CB baboons while helminth infections were relatively more common in WT primates. Some of the parasites observed in this study are reported to be zoonotic in various parasitological literatures. Chemoprophylaxis and other managerial practices were believed to be responsible for the lower worm prevalence in CB primates. Similar intervention against protozoa and other agents will not only improve primate health, but also increase safety to animal handlers and colony workers.