A link between diurnal preference and a variable number tandem-repeat (VNTR) polymorphism in the PERIOD3 gene (PER3) has been demonstrated: the longer PER35 and shorter PER34 alleles with preferences for mornings and evenings, respectively. As many competitive events in South Africa for individual athletes are scheduled for the early mornings, we hypothesized that this might favor those athletes with a preference for morning activities. Self-selected white, male cyclists (CYC, n = 125), runners (RUN, n = 120) and Ironman triathletes (IM, n = 287) of European descent were compared with a control population of active, non-competitive individuals (CON, n = 96). The chronotypes of all CYC, RUN and CON participants and a sub-sample of the IM group (n = 49) were assessed using the Horne–Östberg Morningness–Eveningness Questionnaire, and the PER3 VNTR genotype for each participant was determined. The athlete groups contained more morning-type individuals than the CON group (CYC: 72%, n = 90; RUN: 67%, n = 80; IM: 59%, n = 29; CON: 41%, n = 39; p < .001). The prevalence of the PER35 allele was greater in the athlete groups (CYC: 61%, n = 152; RUN: 58%, n = 132; IM: 56%, n = 324; CON: 38%, n = 76; p < .001), and more athletes were genotyped as PER35/5 than CON individuals (CYC: 41%, n = 51; RUN: 23%, n = 26; IM: 28%, n = 81, CON: 9%, n = 8; p < .001). A strong relationship between chronotype and PER3 VNTR genotype was observed (p < .001). Finally, the time of day at which the athletes preferred to train was related to their chronotype (p < .001). This is the first study of its kind in a South African sporting population, and the results have not yet been replicated. These data suggest that white males of European descent participating in individual endurance sports in South Africa are more likely to be morning types. Furthermore, the PER3 VNTR may be one of the factors contributing to this observation.