Technical Abstract: Understanding the genetic basis of nitrogen and carbon metabolism will accelerate development of plant varieties with high yield and improved nitrogen use efficiency. In this study, we measured the activities of ten enzymes from carbon and nitrogen metabolism and seedling/juvenile biomass in the maize (Zea mays L.) intermated B73×Mo17 (IBM) mapping population, which provides almost a four-fold increase in genetic map distance compared to conventional mapping populations. We found that all ten enzymes are heritable in activity and are positively correlated, indicating they are co-regulated. We also detected negative correlations between biomass and the activity of six enzymes. In total, we found 73 QTL, 8 of which were significant, that influence activity of these ten enzymes and biomass, respectively. While some QTL were shared by different enzymes or biomass, we critically evaluated the probability that this may be fortuitous. All enzyme activity QTL were in trans to the known genomic locations of structural genes, except for single cis-QTL for nitrate reductase, glutamate dehydrogenase, and shikimate dehydrogenase; the low frequency and low additive magnitude compared to trans-QTL indicates that cis-regulation is relatively unimportant versus trans-regulation. We identified two-gene epistatic interactions for eight enzymes and biomass, with three epistatic QTL being shared by two other traits; however, epistasis explained on average only 2.8% of the genetic variance. Overall, this study identifies more QTL at a higher resolution than previous studies of genetic variation in metabolism.