Cerebra cortical areas are populated by the neurons with distinct connecting patterns, underlying the functional specialization of each area. Long association fibers (LAFs) are the neuronal connections between distant areas located in different cortical lobes within a cerebral hemisphere and are critical for higher cortical functions such as integration of sensory inputs of different modalities and regulation of voluntary motions. Recent studies have detected abnormal LAFs in the mental/developmental diseases like schizophrenia and autism spectrum disorders, suggesting the importance of LAFs in cognitive functions. However, how the neuronal circuits of LAFs are organized at cellular level and how the circuits form during cortical development are yet to be revealed. By comparing the gene expression profile of long association neurons (LANs) that project axons through LAFs with that of callosal neurons (CNs) connecting bilateral cerebral hemispheres, we explored the genes preferentially expressed in LANs. Among the candidates obtained, we identified with in situ hybridization (ISH) several genes that show laminar distribution in the adult cerebral cortex, which is a feature of LANs. Double staining with ISH and retrograde tracing from primary motor cortex (M1) to primary somatosensory cortex (S1) confirmed that several among the candidate genes were indeed expressed in LANs. Using the promoters of these LAN-specific genes and tissue clearing methods combined with deep brain imaging, we visualized the entire axon structure of single neurons. We report the results of time-course analysis of axon projections of LANs.