With a new approach we assessed the relative contribution of stored and current carbon compounds to new shoot growth in alpine treeline conifers. Within a free air CO2 enrichment experiment at the alpine treeline in Switzerland, 13C-depleted fossil CO2 was used to trace new carbon in the two tree species Larix decidua L. and Pinus uncinata Ramond over two subsequent years. The deciduous L. decidua was found to supply new shoot growth (structural woody part) by 46% from storage. Surprisingly, the evergreen P. uncinata, assumed to use current-year photosynthates, also utilized a considerable fraction of storage (42%) for new wood growth. In contrast, the needles of P. uncinata were built up almost completely from current-year photosynthates. The isotopic composition of different wood carbon fractions revealed a similar relative allocation of current and stored assimilates to various carbon fractions. Elevated CO2 influenced the composition of woody tissue in a species-specific way, e.g. the water soluble fraction decreased in pine in 2001 but increased in larch in 2002 compared to ambient CO2. Heavy defoliation applied as an additional treatment factor in the second year of the experiment decreased the lipophilic fraction in current-year wood in both species compared to undefoliated trees. We conclude that storage may play an important role for new shoot growth in these treeline conifers and that altered carbon availability (elevated CO2, defoliation) results in significant changes in the relative amount of mobile carbon fractions in woody tissue. In particular, stored carbon seems to be of greater importance in the evergreen P. uncinata than has been previously thought.