BACKGROUND: Tendinopathy pathogenesis is associated with inflammation. Regulatory T (Treg) cells contribute to early tissue repair through an anti-inflammatory action, with the forkhead box P3 (FOXP3) transcription factor being essential for Treg function, and the FC-receptor-like 3 (FCRL3) possibly negatively regulating Treg function. FCRL3 -169T>C and FOXP3 -2383C>T polymorphisms are located near elements that regulate respective genes expression, thus it was deemed relevant to evaluate these polymorphisms as risk factors for tendinopathy development in athletes. METHODS: This case-control study included 271 volleyball athletes (146 tendinopathy cases and 125 controls) recruited from the Brazilian Volleyball Federation. Genotyping analyses were performed using TaqMan assays, and the association of the polymorphisms with tendinopathy evaluated by multivariate logistic regression. RESULTS: Tendinopathy frequency was 63% patellar, 22% rotator cuff and 15% Achilles tendons respectively. Tendinopathy was more common in men (OR = 2.87; 95% CI = 1.67-4.93). Higher age (OR = 8.75; 95% CI = 4.33-17.69) and more years of volleyball practice (OR = 8.38; 95% CI = 3.56-19.73) were risk factors for tendinopathy. The FCRL3 -169T>C frequency was significantly different between cases and controls. After adjustment for potential confounding factors, the FCRL3 -169C polymorphism was associated with increased tendinopathy risk (OR = 1.44; 95% CI = 1.02-2.04), either considering athletes playing with tendon pain (OR = 1.98; 95% CI = 1.30-3.01) or unable to train due to pain (OR = 1.89; 95% CI = 1.01-3.53). The combined variant genotypes, FCRL3 -169TC or -169CC and FOXP3 -2383CT or -2383TT, were associated with an increased risk of tendinopathy among athletes with tendon pain (OR = 2.24; 95% CI: 1.14-4.40 and OR = 2.60; 95% CI: 1.11-6.10). The combined analysis of FCRL3 -169T>C and FOXP3 -2383C>T suggests a gene-gene interaction in the susceptibility to tendinopathy. CONCLUSIONS: FCRL3 -169C allele may increase the risk of developing tendinopathy, and together with knowledge of potential risk factors (age, gender and years playing) could be used to personalize elite athletes' training or treatment in combination with other approaches, with the aim of minimizing pathology development risk.