Introduction: Recurrent subjective complaints may be a result or a cause of worse functioning at school. Interrelations of this type are rarely analysed from the perspective of simultaneously occurring chronic conditions. Method: 5225 students in three age groups (average age 13,59 ±1,66) from the 2017/2018 school year were qualified for the Polish HBSC sample (Health Behaviour in School-aged Children). The occurrence of chronic conditions (CC) and multiple recurrent symptoms (SCL) were analysed jointly. Following groups revealed: CC (-) & SCL (-): 51.5%; CC (-) & SCL (+): 33.5%; CC (+) & SCL (-): 7.1%; CC (+) & SCL (+): 7.9%. Eight aspects of functioning at school were analysed in three subject blocks: general adjustment, social support and bullying. Logistic regression adjusted by gender and grade was applied. Results: The percentage of students qualified to the most positive group CC (-) &SCL (-) is significantly higher among boys than girls and decreases significantly with age. Perception of the school environment becomes significantly worse in the group reporting multiple complaints, regardless of occurrence of chronic conditions. In the group without complaints students with chronic conditions are significantly more likely to experience a higher level of school stress than their healthy peers (p=0.006) and have a slightly worse perception of teacher support (p=0.067). In the multivariate analysis the greatest difference between the CC (-) & SCL (-) and CC (+) & SCL (+) group was determined for being a victim of bullying (OR=4.38) and school stress (OR=3.40). Suffering from a chronic condition clearly modifies the interrelation between perception of school and subjective complaints in the following areas: victimization, school stress and academic achievement. Conclusion: Functioning at school depends on the health of the students and declines in line with increasing health problems, especially in the context of school stress and peer violence. The obtained results ought to be taken into account in the work with the entire class as well as individual work with a student suffering from a chronic disease.