Introduction Although weight loss is common in Parkinson's disease (PD), longitudinal studies assessing weight and body composition changes are limited. Methods In this three-year longitudinal study, 125 subjects (77 PD patients and 48 spousal/sibling controls) underwent clinical, biochemical and body composition assessments using dual-energy X-ray absorptiometry. Results Patients were older than controls (65.6 ± 8.9 vs. 62.6 ± 7.1, P = 0.049), with no significant differences in gender, comorbidities, dietary intake and physical activity. Clinically significant weight loss (≥5% from baseline weight) was recorded in 41.6% of patients, with a doubling of cases (6.5 to 13.0%) classified as underweight at study end. Over three years, patients demonstrated greater reductions in BMI (mean −1.2 kg/m2, 95%CI-2.0 to −0.4), whole-body fat percentage (−2.5% points, 95%CI-3.9 to −1.0), fat mass index (FMI) (−0.9 kg/m2, 95%CI-1.4 to −0.4), visceral fat mass (−0.1 kg, 95%CI-0.2 to 0.0), and subcutaneous fat mass (−1.9 kg, 95%CI-3.4 to −0.5) than in controls, with significant group-by-time interactions after adjusting for age and gender. Notably, 31.2% and 53.3% of patients had FMI Conclusions We found progressive loss of weight in PD patients, with greater loss of both visceral and subcutaneous fat, but not muscle, compared to controls. Several associated factors (motor and non-motor disease features) were identified for these changes, providing insights on possible mechanisms and therapeutic targets.