Four clinical cases regarding the correct diagnosis of early ocular Chlamydia trachomatis (Ct) inflammation, performed by two different modalities on the ocular ecosystem, are discussed. The present study was carried out in parallel using a cotton flock ocular swab and the scraping of upper lid conjunctiva. The ocular samplings were carried out by a first ocular swab from inner canthus and fornix, while the second by a conjunctival scraping from upper the conjunctiva of four patients. In the first case, by ocular swab, all samples resulted negative to Ct-DNA research by PCR, while the cultural analyses showed a growth of saprophytic and opportunist germs in all patients. No growth micetes resulted. On the contrary, in the second case, by conjunctival scraping, three of four samples were positive to Ct-DNA research. No fungal growth was observed, while only the 3rd patient, negative to Ct-DNA research, showed microbial growth. Our study, carried out with two different modalities of sampling on different areas of the same ecosystem, showed different results, demonstrating the importance of sampling accuracy for chlamydial research by molecular analysis in PCR, during the slight phase of inflammation. These initial data indicate that laboratory diagnosis by PCR for precocious Ct infection, not revealed clinically, could represent the first step for a correct diagnostic procedure, eliminating one of the critical points, allowing an accurate, effective and precocious antibiotic therapy. We hypothesize that only by following these correct procedures of sampling during the early phase of chlamydial inflammation, in the future, will it be possible to reduce a pejorative evolution of this worsening disease in people genetically susceptible, building a more efficacious Public Health program of prevention against chronic conjunctivitis and to favour a major prevention of trachoma in endemic areas.