The goal of the research presented in this paper was to study the relations between students' estimation of the real and desired state of family functionality and attendance of religious instruction in school. The results obtained on the sample of 421 secondary school students of the third grade, who opted for attending religious instruction at the beginning of this level of schooling (263 students) or for attending the alternative elective subject - civic education (158 students). For assessing relevant dimensions of the real and desired state of family system functionality, the standardized instruments were used - FACES III (cohesion and flexibility of the family) and F-COPES (strategies of family's overcoming of problems). For collecting data on sociodemographic characteristics of respondents and their families, as well as the assessment of effects of attending religious instruction on the family, we used the Student Questionnaire, constructed for the purposes of this research. Based on the analysis of the obtained results, we reached the conclusion that in certain aspects there are differences in students' assessment of the real and desired state of family functionality, depending on the elective subject they attend, as well as that it can be stated with great probability that some of the measured family characteristics are significantly correlated with the effects of religious instruction on students and their family as a whole.