The main aim of this research was to measure 10th and 12th grade students' biological conceptual understanding and competences through their upper secondary school studies. Data collection started at the beginning of the upper secondary school biology studies in the 10th grade. The same students participated in this research when they were in the 12th grade. A validated instrument of covering four competences: biological conceptual understanding, problem-solving, critical thinking and divergent thinking was used. Overall, this research was meant to evaluate students' conceptual understanding and cognitive skills (problem-solving, critical thinking, divergent thinking) through the socio-scientific issue of lactose intolerance. The sample of students was formed from 42 representatively chosen Estonian schools of grade 10 (N=967) and grade 12 (N=802). The development conceptual understanding and competences of students' during three upper secondary school years of biology studies were discussed. The main results showed that during three years of schooling the students exhibited a statistically significant increase in the tasks, that measured students' biological understanding and cognitive skills. The results showed that the students achieved lower scores in tasks that measured their decision-making and socio-scientific reasoning skills.