Gene-chip as a very useful means of biotechnology has been applied to many research areas such as gene discovery, disease diagnosis and pharmacogenomics etc. , but commercially available gene-chip detection instruments are too expensive to be accepted by common labs. In this paper, a laser confocal scanning system with holographic notch filters used for simple gene-chip detection is presented. The system is mainly composed of an ordinary optical microscope, two holographic notch filters, a He-Ne laser, a digital controlled X-Y platform, a photodetector and a PC. The volume holographic notch filters were fabricated in our lab to substitute for the expensive narrow-band interference excitation filter and the dichroic filter in the conventional confocal detection system. The detection experiment was carried out on the gene-chips hybridized with cy5-labeled targets and the system sensitivity was determined by static measurement. The sensitivity is about 2x10-22mol/µm2, and the resolution is 10µm. The results indicate that the system can be used in primary gene-chip detection.