Chlamydia trachomatis is a pathogen of humans that infects urogenital tract (UGT) and ocular mucosal surfaces. UGT C. trachomatis is a common cause of sexually transmitted infection. Trachoma is an ocular infection characterised by frequent non-sexual transmission in childhood, and hypersensitivity reactions that eventually can lead to anatomical changes and possible blindness. It is known that serovars A, B, Ba and C are associated with trachoma and rarely observed in urogenital infections. Genomic studies have shown that the trachoma serovars define a phylogenetic lineage. Australia is the only developed country with endemic trachoma, where it persists in remote Aboriginal communities. Studies in the north of the Northern Territory (NT) in the 1980s-1990s showed association of trachoma serovars with ocular site of isolation and signs consistent with trachoma, although serovar B isolates were also frequent in UGT specimens. Remarkably, genome sequencing showed that these ocular isolates had the appearance of urogenital strains that had acquired by recombination the ompA alleles that confer the serovar phenotypes. This does not support the model that trachoma strains form a coherent phylogenetic lineage. Child protection implications relate to whether C. trachomatis positive UGT samples from young children could be accounted for by autoinoculation from trachoma, or must be regarded as highly indicative of sexual contact. The high frequency presence of trachoma serovars in UGT specimens in the NT in the 1980s-1990s suggests that drawing conclusions concerning the origin of a C. trachomatis strain on the basis of serovar/genotype is not reliable. However a much more recent survey has failed to find trachoma serovars in UGT specimens from the NT, suggesting that genotyping is a more reliable indicator of the origin of a C. trachomatis strain than it was 25 years ago. A model for C. trachomatis surveillance, and inference of confidence limits for probabilities of whether strains in specimens from young children are from ocular or UGT infections will be described in detail. A key assumption is that any excess of trachoma serovars/genotypes observed in UGT specimens from young children as compared to the frequency in UGT specimens in adults is an indicator of the proportion of trachoma genotypes in UGT specimens from young children that can be accounted for by autoinoculation from an ocular source.