Photosynthetic performance and root respiration were measured for seedlings of Scots pine and Norway spruce under constant conditions in an open gas exchange system in the laboratory. Measurements were carried out after root exposure to ‐20, ‐5 and 0°C and subsequent longtime storage in darkness at +1 or +4°C. Stomatal conductance in relation to net photosynthetic rates was also investigated after the same treatment of seedlings. Root respiration was low for seedlings whose root system had been exposed to ‐20°C, Scots pine showing lower rates than Norway spruce. This was probably an indication of root damage. At least for one provenance of Scots pine, respiration rates were higher for seedlings stored at +1 than at +4°C. Photosynthetic performance was also lowest for seedlings whose roots had been exposed to +20°C compared to higher temperatures, the difference being more clear‐cut for Norway spruce than for Scots pine. Storage at +1 gave slightly higher photosynthetic rates than at +4°C. There was a close relation between stomatal conductance measured on individual needles and photosynthetic performance measured on the whole seedling.