We focus on two types of centralised national examinations (the 10th grade tests and Matura examination) that are being carried out in Lithuania for two decades. The aim of the paper is to analyse assessments of mathematics for the entire Lithuanian secondary school population that have no sampling errors while considering the factors of location, school ownership and gender as important indicators when judging about educational effectiveness in terms of quality and equity. We analyse the results of the 10th grade tests for the 2011–2015 period and the results of the same cohorts participating in the Matura examination. We observe that the distribution of the assessments of both exams is asymmetric with a positive skew. The median often is below the middle of the grade scale indicating poor performance or mismatch between knowledge and examination tasks. There are limited differences in assessments with respect to gender and school location, although we detect a tendency to have better mathematics achievement in private schools. The conclusions drawn from national assessment data is somewhat different from international data thus one cannot neglect national information for the development of educational policy. The variables analysed in the analysis has limited predictive power for achievements in mathematics and further analysis is called-for.