A molecularly imprinted silica (MIS) coupled to a microwave sensor was used to detect three fungicides (iprodione, procymidone and pyrimethanil) present in most French wines. Chemometric methods were applied to interpret the microwave spectra and to correlate microwave signals and fungicide concentrations in a model wine medium, and in white and red Burgundy wines. The developed microwave sensor coupled to an MIS and to its control, a nonimprinted silica (NIS), was successfully applied to detect the three fungicides present in trace levels (ng L-1) in a model wine. The MIS sensor discriminated the fungicide concentrations better than the NIS sensor. Partial Least Squares models were suitable for determining iprodione in white and red wines. A preliminary method validation was applied to iprodione in the white and red wines. It showed a limit of detection (LOD) lower than 30 ng L-1 and a recovery percentage between 90 and 110% when the iprodione concentration was higher than the LOD. The determined concentrations were below the authorized level by far.