We estimated sibling resemblance in health-related physical fitness (PF) and examined how individual characteristics and shared natural environment accounted for sibling similarities. The sample comprised 656 sibling pairs and 102 triplets (6–15 years of age), from three geographical areas of Peru. PF components included morphological (waist circumference, sum of skinfolds), muscular (handgrip strength, standing long jump), and motor (shuttle-run). Body mass index (BMI) and somatic maturation were also assessed. In general, sibling intraclass correlations differed significantly across sib-ship types for waist circumference and handgrip strength but were the same for sum of skinfolds, standing long jump, and shuttle-run. Further, in general, both individual characteristics and geographical area of residence significantly influenced the magnitude of sibling resemblance as well as the mean levels of PF. In conclusion, individual characteristics and shared natural environment jointly influenced the expression of PF in Peruvian siblings, revealing the importance of these features when designing individualized programs promoting fitness.