During the glyoxysomal beta-oxidation of long-chain acyl-CoAs, short-chain intermediates accumulate transiently (Kleiter and Gerhardt 1998, Planta 206: 125-130). The studies reported here address the underlying factors. The studies concentrated upon the aspects of (i) chain length specificity and (ii) metabolic regulation of the glyoxysomal beta-oxidation of sunflower (Helianthus annuus L.) cotyledons. (i) Concentration-rate curves of the beta-oxidation of acyl-CoAs of various chain lengths showed that the beta-oxidation activity towards long-chain acyl-CoAs was higher than that towards short-chain acyl-CoAs at substrate concentrations <20 mu M. At substrate concentrations >20 mu M, long-chain acyl-CoAs were beta-oxidized more slowly than short-chain acyl-CoAs because the beta-oxidation of long-chain acylCoAs is subject to substrate inhibition which had already started at 5-10 mu M substrate concentration and results from an inhibition of the multifunctional protein (MFP) of the beta-oxidation reaction sequence. However, low concentrations of free long-chain acyl-CoAs are rather likely to exist within the glyoxysomes due to the acyl-CoA-binding capacity of proteins. Consequently, the beta-oxidation rate towards a parent long-chain acyl-CoA will prevail over that towards the short-chain intermediates. (ii) Low concentrations (15 mu M) of a long-chain acyl-CoA exerted an inhibitory effect on the beta-oxidation rate of butyryl-CoA. Reversibility of the inhibition was observed as well as metabolization of the inhibiting long-chain acyl-CoA. Regarding the activities of the individual beta-oxidation enzymes towards their C-4 substrates in the presence of a long-chain acyl-CoA, the MFP activity exhibited strong inhibition. This inhibition appears not to be due to the detergent-like physical properties of long-chain acylCoAs. The results of the studies, which are consistent with the observation that short-chain intermediates accumulate transiently during complete degradation of a long-chain acyl-CoA, suggest that the substrate concentration-dependent chain-length specificity of the beta-oxidation and a metabolic regulation at the level of MFP are factors determining this transient accumulation.