We report a microfibre absorption sensor by using a 900 nm diameter silica microfibre embedded in a 125 μm wide microchannel with a detection length of 2.5 cm. Investigated by measuring the absorbance of methylene blue (MB), the sensor shows a detection limit down to 50 pM with excellent reversibility in a concentration range of 0–5 nM. The sensor has also been applied to bovine serum albumin (BSA) measurement, with a detection limit of 10 fg mL−1. In addition, the sample volume requirement is merely 500 nL with a probing light power of about 150 nW, which is very promising for safe detection of single or a few molecules of biological specimens.