In the present study we evaluated the anti-Toxoplasma gondii immunoglobulin profiles of a group of 118 individuals living in an endemic area. The aim of the study was to select biomarkers to support the ophthalmological diagnosis of retinal/retinochoroidal scars presumably caused by T. gondii infection. Overall anti-T. gondii reactivity of the IgM, IgG, IgA, IgE and IgG subclasses was investigated by flow cytometry-based anti-fixed tachyzoite antibodies (FC-AFTA) in four groups of subjects, referred to as: i) TOXO(L) — seropositive patients with retinal/retinochoroidal scars presumably caused by T. gondii infection; these patients were further subdivided according to morphological aspects of their ocular scar lesions as A, B or C; ii) TOXO(NL) — seropositive patients without ocular scar lesions; iii) NEG(L) — T. gondii seronegative patients presenting retinal lesions; and iv) NEG(NL) — T. gondii seronegative without retinal lesions (negative controls). Our data demonstrated that anti-T. gondii IgG profiles were able to discriminate the mean reactivity of TOXO(L) from all other clinical groups. Analysis of anti-T. gondii immunoglobulin profiles revealed that IgM and IgG were good biomarkers capable of discriminating between individual reactivity in patients with retinal/retinochoroidal scars presumably caused by T. gondii infection [TOXO(L)] from those caused by other clinical conditions. Furthermore, anti-T. gondii IgG1 reactivity was able to discriminate TOXO(L) from all other clinical groups. In conclusion, the pre-selected IgM, IgG and IgG1 anti-T. gondii antibody subclasses were able to segregate both TOXO(L) and the other subgroups, including the scar lesion group types (A, B, C), from other clinical conditions. These results suggest the applicability of this technique in the clinical laboratory to detect putative biomarker for diagnosis of ocular lesions in T. gondii-infected patients. Studies in other areas implementing the methods described in the present study would be of value and enable evaluation of a system for classification of presumed ocular toxoplasmosis scar lesions. This classification would make comparative studies on ocular toxoplasmosis conducted in different regions around the world possible.