The association of infectious burden of Chlamydia trachomatis with patient characteristics and clinical disease may have implications for understanding disease pathogenesis. We examined chlamydial load from 171 urine samples where load was based on copy number of organisms per copy number of eukaryotic cells derived by real-time quantitative PCR. High- (E, F, G) and low-prevalence (Ia, H, J, Ja) genotypes in the population had similar loads, suggesting a similar propensity for replicating in vivo, despite their differential ecological success. Symptomatic and asymptomatic patients also had similar chlamydial loads, indicating that virulence differences are likely not associated with variations in replication. There was a significant difference in genotypes by age for F (<31 years; P = 0.031) and for H where the mean age was lower than for the most prevalent genotype, E (P=0.013). Also, men had a significantly lower load than women when the genotype was F (P=0.042), although there was no significant difference in load between partners. Patients with recurrent chlamydial infections had a significant reduction in load with each subsequent episode regardless of genotype (P=0.007), suggesting that immune defenses do not block chlamydial entry but may impact replication. Additionally, the probability of being infected with J was 7.7-fold higher in patients with prior chlamydial infections (P=0.016), and although the loads were lower when compared with patients without prior infection, the results did not reach statistical significance. These findings suggest that chlamydial burden could be an important marker for recurrence and host immune response, which would facilitate pathogenesis research.