Aim To investigate changes in bone and cartilage tissue during the use of non-steroidal anti-inflammatory drugs and paracetamol in experimental osteoarthritis and hypothyroidism by the markers CTX-I and CTX-II. Methods The experiments were performed on 75 white nonlinear rats of both sexes, which recreated osteoarthritis and hypothyroidism. Experimental osteoarthritis was performed by single intra-articular administration of monoiodoacetic acid solution in the knee joint and experimental hypothyroidism was reconstructed by enteral administration of a solution of carbimazole. After the formation of the experimental models on the 42 day of the experiment, the animals were divided into 14 groups and drug administration began daily for 5 days. The quantitative level of markers of blood serum was performed by specific kits, which are based on ELISA on 42 and 47 days of the experiment. Results The degree of influence on degenerative-dystrophic processes in bone tissue, which was assessed by the level of the marker СTX-I in the serum of rats, the studied drugs were as follows: diclofenac sodium > ibuprofen > nimesulide = meloxicam > celecoxib > paracetamol. According to the degree of influence on degenerative-dystrophic processes in cartilage tissue, which were assessed by the level of marker СTX-II in the serum of rats, the studied drugs were as follows: nimesulide > celecoxib > meloxicam > ibuprofen > diclofenac sodium > paracetamol. Conclusion Determination of the levels of CTX I and СTX II allows the evaluation of the bone and cartilage condition in experimental osteoarthritis and hypothyroidism.Copyright© by the Medical Assotiation of Zenica-Doboj Canton.