In this work the preparation of polyamide 12 (PA12) based composites reinforced with pristine and surface-modified carbon nanotubes is reported. A qualitative and quantitative evaluation of multi-walled carbon nanotube functionalization with oxygen containing reactive groups achieved by different procedures of chemical treatment is presented. Simple strong oxidative acid treatment as well as chlorination with subsequent chloroacetic acid treatment were applied. Carbon nanotubes (CNTs) were also subjected to chlorine and ammonia in gaseous atmosphere with small differences in after-ammonia treatment. Commercial COOH-functionalized carbon nanotubes were compared with nanotubes that were laboratory modified. The effect of CNT functionalization was evaluated basing on the improvement of mechanical and thermal properties of polyamide 12 composites prepared by in situ polymerization. It was found that high concentration of oxygen-containing functional groups on nanotube surface is not sufficient to improve the composite performance if the structure of carbon nanotubes is defective. Indeed, the best effects were achieved for composites containing nanotubes modified under mild conditions, seemingly due to a compromise between morphology and surface chemical structure.