Comparative results of baseline and endpoint screening for intestinal parasites are reported from Javanese men enrolled in a year-long, placebo-controlled malaria prophylaxis trial in Irian Jaya. The objective was to detect nontarget qualitative changes that may have resulted from prolonged chloroquine (300 mg base weekly) or primaquine (0.5 mg base/kg daily) prophylaxis. Fresh fecal specimens were examined (blinded trial) for parasites and ova using a modified Kato-Katz thick smear method. More than 88% (94/106) of the baseline population was infected by 1 or more parasite species of which hookworm and Blastocystis hominis were dominant. Paired comparison between baseline and endpoint revealed no significant changes within the primaquine or chloroquine groups with regard to the variety of species found, the mean number of species or ova/subject, the relative proportion of infections caused by these species, or the occurrence of parasite-free, single, and multiple infections. Relative to placebo, there was a significantly greater proportion of infections by Entamoeba histolytica/dispar and a lower mean hookworm egg count in the chloroquine group. The endpoint proportion of new or increased infections in the primaquine group was significantly lower than that of the chloroquine group but comparable to that of the placebo. Despite the dosage employed, the frequency and duration of use, and excretion primarily through the bowels as the active parent compound, primaquine appeared to have little or no significant effect against a variety of common intestinal parasites. These largely negative results lend support for the safety and acceptability of primaquine as a daily malaria prophylactic in a population frequently at risk of intestinal helminth infections.