In recent years, second harmonic generation (SHG) microscopy has revolutionised the field of biological imaging by offering a new means of visualising the fine structures of collagen tissues with excellent image penetration while minimising photodamage. This project involves the design and construction of a SHG microscope that is built around a compact femtosecond fibre laser for collagen imaging. Operating at 1032 nm, the microscope has demonstrated a penetration depth of beyond 320 microns in collagen, which is considerably superior to depths of 250 to 300 microns achievable with a conventional SHG microscope coupled to a Ti:sapphire excitation laser. The imaging characteristics of the microscope have been tested with a modified sample of bovine pericardium. The results indicate the microscope is polarisation-sensitive to the tissue structure and is capable to detecting signal changes at 10 μm resolution. This thesis will describe in detail, to our best knowledge, the first SHG microscope equipped with a compact and robust all-fibre femtosecond 1032 nm laser source.