Nanocrystals of α,ω-alkanedicarboxylic acids (HO 2C(CH 2) n-2CO 2H, n = 3-13, odd) grown in aligned nanometer-scale cylindrical pores of nanoporous poly(cyclohexylethylene) monoliths (p-PCHE) adopt preferred orientations relative to the pore direction. X-ray diffraction reveals that nanocrystals of malonic acid (n = 3) grown in 14, 30, and 40 nm diameter pores adopted two preferred mutually perpendicular orientations simultaneously, each orientation coinciding with the direction of hydrogen-bonded chains in the solid state. Nanocrystals of glutaric acid (n = 5) embedded within 30 and 40 nm pores adopted orientations with hydrogen-bonded chains coincident with the pore direction, but the chains were perpendicular to the pore direction in 14 nm pores. Pimelic acid (n = 7) nanocrystals were oriented with their hydrogen-bonded chains parallel to the pore direction, but nanocrystals of longer alkane dicarboxylic acids (n = 9, 11, or 13) adopted orientations in which the their hydrogen-bonded chains progressively tilted away from the pore direction as the alkane length was increased. This behavior can be attributed to increasingly strong dispersive interactions between the alkane chains, which alter the ranking of the fast growing crystal directions. The appearance of preferred orientations for embedded nanocrystals argues that critical size effects and surface energy considerations favor precritical nuclei that are oriented with their fast growth axis aligned with the pore direction. This condition permits the nuclei to achieve critical size more readily while minimizing the area of planes with high surface energies, thereby providing a competitive advantage over other orientations during nucleation. The observation in some cases of two orientations simultaneously and size-dependent orientations reveals the delicate balance of free energies among differently oriented nuclei. Collectively, these observations demonstrate the utility of nanoscale confinement for investigating the earliest stages of crystal growth.