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Prostate cancer (PCa) incidence has steadily increased in Sweden, more steeply in the mid-1990s caused by increased opportunistic prostate-specific antigen (PSA) testing. Tallness, normal weight, and non-smoking are associated with more PSA testing, which increases detection of low-risk and localised PCa. We investigated time trends of height, body mass index (BMI), and smoking with PCa risk in 171,889 men in Sweden aged 50–64 years at baseline, who were linked to nationwide cancer registers during follow-up. Cox regression determined the association of these factors assessed before 1980, 1980–1994, and 1995–2004 with PCa risk. During 15 follow-up years, 8,049 men were diagnosed with PCa. The association of height with PCa was weakly positive across all calendar periods. For obesity (BMI ≥30 kg/m2) vs. normal weight (BMI 18.5–24.9 kg/m2) and current vs. never smoking, the associations changed from null before 1980 (HR 1.03, 95% CI 0.86–1.23, and 1.11, 95% CI 0.97–1.27) to negative in 1995–2004 (HR 0.83, 95% CI 0.74–0.93, and 0.86, 95% CI 0.79–0.93; pinteraction between periods = 0.05 and 0.001). In men with clinical characteristics available, height was positively associated with both aggressive and non-aggressive PCa whilst obesity and smoking showed negative associations only with non-aggressive PCa. These findings likely reflect differences in PSA testing by BMI and smoking habits and contribute important knowledge for etiological studies of PCa.