Studies on the effects of antipsychotics on cognitive deficits in schizophrenia mostly suggest a superior effect of atypical over typical compounds, although findings are inconsistent and effect sizes small. Several methodological issues such as heterogenous patient samples, incomparable drug doses, effects of prior medication, construct validity and retest effects on neuropsychological tasks confound most results and the comparability between studies. Consequently, the conclusion concerning effects of antipsychotics on cognition is still equivocal. Objective: The present randomised clinical trial examined the effects on cognition of comparatively low doses of a typical antipsychotic (zuclopenthixol) and an atypical antipsychotic (risperidone) in a homogenous group of drug-naïve first episode schizophrenic patients in a longitudinal setting. Methods: First-episode schizophrenic patients who had never previously been exposed to antipsychotic treatment (N=25) were randomly allocated to treatment with flexible doses of zuclopenthixol or risperidone in an open label design. Cognitive functions were examined both when patients were drug-naive, and after 13 weeks of treatment. A comprehensive neuropsychological battery was used in order to optimise construct validity, and principal components of cognitive functions were extrapolated in order to reduce Type I errors. A healthy control group was tested at baseline and after 13 weeks, in order to examine retest effects. The cognitive domains studied were executive functions, selective attention, and reaction time. Results: The patients showed considerable cognitive deficits when drugnaïve. There were few differential effects of risperidone and zuclopenthixol on cognitive deficits, except for a differential significance respectively tendency towards improved reaction and movement times in the risperidone group, and a lack of such in the zuclopenthixol group. These differences were no longer significant after covarying for EPS and anticholinergic medication that were more prevalent in the zuclopenthixol group, and the increases after medication were comparable to retest effects in controls. Conclusion: The study underscores the importance of examining impact of factors such as clinical improvement, EPS, anticholinergic medication and retest effects in longitudinal efficacy studies. This study does not support efficacy of either risperidone or zuclopenthixol on cognitive functions in drug-naïve schizophrenic patients after 3 months of medication, because neither could be distinguished from retest effects of the healthy control group.