Skeletal muscle responds to exercise by a diversity of processes that collectively contribute to short-term and structural adaptations to the demanded performance capacities. There is common consensus that, in general, adequate nutrient availability during and after exercise is important to maximise skeletal muscle adaptation and ultimately performance. At the same time, several knowledge gaps remain regarding the precise mechanisms underlying these effects on adaptation, the most optimal nutrient composition in relation to type of exercise, optimal timing etc. This dissertation addresses some of these unsolved issues by studying the role of carbohydrates and proteins during adaptation following different forms of exercise. The first part (chapters 2 – 4) focusses on carbohydrate availability with resistance exercise, whereas the second part (chapters 5 - 7) specifically addresses the effects and potential of protein supplementation with endurance training. In chapter 2 we reviewed the existing literature regarding the role of skeletal muscle glycogen with endurance and resistance exercise. Based on this review we concluded that the role of muscle glycogen levels and/or carbohydrate availability on the skeletal muscle adaptive response to resistance exercise requires further scientific attention. To experimentally explore this, we assessed the impact of a pre-exercise meal that differed in macronutrient content on skeletal muscle glycogen levels and acute transcriptional level analysing specific mRNAs in the post-resistance exercise period in chapter 3. Specifically, after a glycogen depleting endurance exercise session in the morning, subjects received an isocaloric mixed meal containing different amounts of carbohydrates and fat 2 hours before a resistance exercise session in the afternoon, while ample protein was provided throughout the day. We hypothesized that some of the selected mRNAs associated with substrate metabolism and mitochondrial biogenesis would differ between the nutritional conditions, without any changes in proteolytic genes. The findings described in chapter 3 demonstrated that muscle mRNA responses related to exercise adaptation were minimally affected by the pre-exercise meals that differed in macronutrient composition. In chapter 4, derived from the same study, we describe the analysis of a number of plasma cytokine patterns during the day to investigate whether these mediators were affected by carbohydrate availability. We hypothesized that some selected cytokines would differ between nutritional conditions, whereas other circulating cytokines suggested to be involved in skeletal muscle adaptation would not respond differently. Our main finding was that a pre-exercise meal in general did not influence plasma cytokine responses in the post-resistance exercise period. Findings of chapter 3 and 4 contribute to the view that carbohydrate availability during resistance exercise is of minor importance when aiming for an acute positive skeletal muscle adaptive response. In addition, our data question the importance of carbohydrates as both substrate for resistance exercise and as modulator of the skeletal muscle response that underlies adaptation. Yet, at present it might be premature to change carbohydrate recommendations for individuals performing resistance exercise. Shifting our focus to proteins, we first reviewed the effects and possible underlying physiological mechanisms of protein supplementation on the adaptive response to endurance training in Chapter 5. To further explore these insights, we performed a double-blind randomised controlled trial with repeated measures to determine whether protein supplementation impacts the adaptive response to endurance training. In chapter 6 we provide proof-of-concept that protein supplementation elicited greater increases in VO2max and stimulated lean mass gain in response to prolonged endurance training. To our knowledge, this was the first double-blind randomised controlled trial with repeated measures showing that protein supplementation enhances the adaptive response to endurance training. These remarkable effects of protein on VO2max that were observed give rise to questions regarding their underlying mechanisms. To this end, we analysed the muscle transcriptome to gain insight into changes in the steady-state gene expression. In chapter 7, we demonstrated that prolonged endurance training changed expression of genes involved in extracellular matrix organisation, energy metabolism and oxidative phosphorylation. Changes in extracellular matrix organisation tended to be greater in the protein group than in the control group and these greater transcriptional changes may reflect the enhanced physiological adaptation as a result of protein supplementation.