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Purpose: It has been hypothesized that isolated human communities are particularly favourable for identifying genetic variants underlying complex human traits and diseases because of their reduced genetic and environmental diversity. The aim of this study was to identify genomic loci that may control variation in visual quantitative traits in 1,057 examinees in isolated island of Vis, Croatia, by positional cloning. Methods: Using refractometer, ultrasound and Canon CR-DGI non-mydriatic fundus retinal camera we obtained a number of visual quantitative and qualitative traits in our set of examinees. All measurements have been adjusted for potential confounders that were identifyied through an appropriate questionnaire. Both linkage analysis and and genome-wide association approach were used (PLINK and GENABEL softwares) to identify genomic loci that may have significant contribution to the variation observed in those traits. Results: A number of loci have been identified in the genome that approached formal significance levels after Bonaferroni correction of 10-6. Those loci now require repeat in other populations to eliminate false positive findings, and further study in bioinformatics and functional genomics to understand their potential role in trait variation and possible development of pathological states. Conclusions: This study showes that mapping genetic variants underlying complex human traits in isolated population is a feasible and powerful approach. We aim to expand our studies to other Croatian islands to further increase the power of the study.