Nonfluorescent labels were used for an array-format multiplex detection of alternative splice junctions of breast cancer susceptibility gene 1 (BRCA1) by surface-enhanced Raman scattering (SERS). A four-plex detection scheme using nonfluorescent labels was demonstrated for DNA sequences specific to four BRCA1 alternative splice variants:  Δ(11q) (the last 3309 nt deleted from exon 11), Δ(9, 10) (exon 9 and 10 deleted), Δ(5) (exon 5 deleted), and Δ(5q, 6) (the last 22 nt of exon 5 and the entire exon 6 is deleted). This is the first proof-of-concept study to apply SERS-based detection using nonfluorescent labels to investigate alternative gene splicing. Detection sensitivity of up to 1 fM was demonstrated for the Raman labels chosen to clearly discriminate the splice junctions via specific target identification. The proposed approach has the potential to become a highly sensitive and selective tool for comprehensive alternative splicing profiling of BRCA1 or other genes relevant to specific diseases.