A method for detection of multiple target sequences from a target nucleic acid and/or genetic analysis of a target nucleic acid in a sample, comprising: (a) optionally releasing, isolating or concentrating the nucleic acids present in the sample; (b) amplifying one or more regions of the target nucleic acid present in the sample with one or more suitable primer pairs, said one or more regions of the target nucleic acid comprising the target sequences to which the oligonucleotide probes hybridize; (c) performing a first hybridization reaction with the amplification products obtained in step (b) and a combination of at least two pools of oligonucleotide probes, wherein the oligonucleotide probes specifically hybridize to a target sequence from the target nucleic acid, wherein the oligonucleotide probes are capable of hybridizing to the amplification products under the same hybridization and wash conditions, and wherein said pools of oligonucleotide probes are immobilized to a known location on a first support; (d) detecting the hybrids formed in step (c); (e) performing a second hybridization reaction with the relevant amplification products obtained in step (b) and a combination of the oligonucleotide probes that are present in the pool(s) of oligonucleotide probes for which a positive hybridization signal was detected in step (d), wherein said oligonucleotide probes are individually immobilized to a known location on one or more second support(s); (f) detecting the hybrids formed in step (e); and (g) inferring the presence of at least one of the multiple target sequences from the target nucleic acid in the sample and/or the genotype of the target nucleic acid present in the sample from the differential hybridization signal(s) obtained in step (f). (a) optionally releasing, isolating or concentrating the nucleic acids present in the sample; (b) amplifying one or more regions of the target nucleic acid present in the sample with one or more suitable primer pairs, said one or more regions of the target nucleic acid comprising the target sequences to which the oligonucleotide probes hybridize; (c) performing a first hybridization reaction with the amplification products obtained in step (b) and a combination of at least two pools of oligonucleotide probes, wherein the oligonucleotide probes specifically hybridize to a target sequence from the target nucleic acid, wherein the oligonucleotide probes are capable of hybridizing to the amplification products under the same hybridization and wash conditions, and wherein said pools of oligonucleotide probes are immobilized to a known location on a first support; (d) detecting the hybrids formed in step (c); (e) performing a second hybridization reaction with the relevant amplification products obtained in step (b) and a combination of the oligonucleotide probes that are present in the pool(s) of oligonucleotide probes for which a positive hybridization signal was detected in step (d), wherein said oligonucleotide probes are individually immobilized to a known location on one or more second support(s); (f) detecting the hybrids formed in step (e); and (g) inferring the presence of at least one of the multiple target sequences from the target nucleic acid in the sample and/or the genotype of the target nucleic acid present in the sample from the differential hybridization signal(s) obtained in step (f).