The determination of the oxygen isotope composition of diatom silica in sediment cores is important for paleoclimate reconstruction, especially in non-carbonate sediments, where no other bioindicators such as ostracods and foraminifera are available. Since most currently available analytical techniques are time-consuming and labour-intensive, we have developed a new, safer, faster and semi-automated online approach for measuring oxygen isotopes in biogenic silica. Improvements include software that controls the measurement procedures and a video camera that remotely records the reaction of the samples under BrF5 with a CO2 laser. Maximum safety is guaranteed as the laserfluorination unit is arranged under a fume hood in a separate room from the operator. A new routine has been developed for removing the exchangeable hydrous components within biogenic silica using ramp degassing. The sample plate is heated up to 1100°C and cooled down to 400°C in ~7 h under a flow of He gas (the inert Gas Flow Dehydration method - iGFD) before isotope analysis. Two quartz and two biogenic silica samples (~1.5 mg) of known isotope composition were tested. The isotopic compositions were reproducible within an acceptable error; quartz samples gave a mean standard deviation of <0.15%(1σ) and for biogenic silica <0.25%(1σ) for samples down to ~0.3 mg. The semiautomated fluorination line is the fastest method available at present and enables a throughput of 74 samples/week. © 2010 John Wiley & Sons, Ltd.