Batch-effects present challenges in the analysis of high-throughput molecular data and are particularly problematic in longitudinal studies when interest lies in identifying genes/features whose expression changes over time, but time is confounded with batch. While many methods to correct for batch-effects exist, most assume independence across samples; an assumption that is unlikely to hold in longitudinal microarray studies. We propose B atch effect R eduction of m I croarray data with D ependent samples usin G E mpirical Bayes ( BRIDGE ), a three-step parametric empirical Bayes approach that leverages technical replicate samples profiled at multiple timepoints/batches, so-called “bridge samples”, to inform batch-effect reduction/attenuation in longitudinal microarray studies. Extensive simulation studies and an analysis of a real biological data set were conducted to benchmark the performance of BRIDGE against both ComBat and longitudinal ComBat . Our results demonstrate that while all methods perform well in facilitating accurate estimates of time effects, BRIDGE outperforms both ComBat and longitudinal ComBat in the removal of batch-effects in data sets with bridging samples, and perhaps as a result, was observed to have improved statistical power for detecting genes with a time effect. BRIDGE demonstrated competitive performance in batch effect reduction of confounded longitudinal microarray studies, both in simulated and a real data sets, and may serve as a useful preprocessing method for researchers conducting longitudinal microarray studies that include bridging samples.