The heart's mechanical activity can be appraised by auscultation recordings, taken from the 4-Standard Auscultation Areas (4-SAA), one for each cardiac valve, as there are invisible murmurs when a single area is examined. This paper presents an effective approach for cardiac murmur detection based on adaptive neuro-fuzzy inference systems (ANFIS) over acoustic representations derived from Empirical Mode Decomposition (EMD) and Hilbert-Huang Transform (HHT) of 4-channel phonocardiograms (4-PCG). The 4-PCG database belongs to the National University of Colombia. Mel-Frequency Cepstral Coefficients (MFCC) and statistical moments of HHT were estimated on the combination of different intrinsic mode functions (IMFs). A fuzzy-rough feature selection (FRFS) was applied in order to reduce complexity. An ANFIS network was implemented on the feature space, randomly initialized, adjusted using heuristic rules and trained using a hybrid learning algorithm made up by least squares and gradient descent. Global classification for 4-SAA was around 98.9% with satisfactory sensitivity and specificity, using a 50-fold cross-validation procedure (70/30 split). The representation capability of the EMD technique applied to 4-PCG and the neuro-fuzzy inference of acoustic features offered a high performance to detect cardiac murmurs.