A method for multiplexed assembly of two or more predefined nucleic acid fragments in multiple reaction compartments comprising the following steps: (a) designing a plurality of oligonucleotide sequences together comprising the sequences of the two or more predefined nucleic acid fragments and synthesizing the oligonucleotides to obtain a plurality of single-stranded oligonucleotides, (b) selectively retrieving a first and a second and further sub-sets of the plurality of single-stranded oligonucleotides, wherein the oligonucleotides of each sub-set are components of two or more predefined nucleic acid fragments, and wherein all oligonucleotides belonging to one of the two or more predefined nucleic acid fragments share a region of sequence complementarity with at least one other oligonucleotide belonging to the same nucleic acid fragment, (c) pooling the oligonucleotides of the first sub-set into a first reaction compartment, the second sub-set into a second reaction compartment and pooling the further sub-sets into further reaction compartments, wherein the number of reaction compartments is between 10 and 500, and (d) simultaneously assembling under suitable conditions the two or more nucleic acid fragments in the first, second and further reaction compartments, wherein pooling the sub-sets of oligonucleotides comprises (i) grouping the first, second and further sub-sets of oligonucleotides according to fragment GC content, optionally wherein the two or more nucleic acid fragments assembled in each reaction compartment do not deviate by more than 10% in GC content, (ii) grouping the first, second and further sub-sets of oligonucleotides according to fragment length, optionally wherein the two or more nucleic acid fragments assembled in each reaction compartment do not deviate by more than 10% in length, and (iii) grouping the first, second and further sub-sets of oligonucleotides according to fragment similarity such that the two or more nucleic acid fragments assembled in the same reaction compartment are non-similar, and optionally, wherein the single-stranded oligonucleotides are not amplified prior to the pooling and/or assembly. (a) designing a plurality of oligonucleotide sequences together comprising the sequences of the two or more predefined nucleic acid fragments and synthesizing the oligonucleotides to obtain a plurality of single-stranded oligonucleotides, (b) selectively retrieving a first and a second and further sub-sets of the plurality of single-stranded oligonucleotides, wherein the oligonucleotides of each sub-set are components of two or more predefined nucleic acid fragments, and wherein all oligonucleotides belonging to one of the two or more predefined nucleic acid fragments share a region of sequence complementarity with at least one other oligonucleotide belonging to the same nucleic acid fragment, (c) pooling the oligonucleotides of the first sub-set into a first reaction compartment, the second sub-set into a second reaction compartment and pooling the further sub-sets into further reaction compartments, wherein the number of reaction compartments is between 10 and 500, and (d) simultaneously assembling under suitable conditions the two or more nucleic acid fragments in the first, second and further reaction compartments, (i) grouping the first, second and further sub-sets of oligonucleotides according to fragment GC content, optionally wherein the two or more nucleic acid fragments assembled in each reaction compartment do not deviate by more than 10% in GC content, (ii) grouping the first, second and further sub-sets of oligonucleotides according to fragment length, optionally wherein the two or more nucleic acid fragments assembled in each reaction compartment do not deviate by more than 10% in length, and (iii) grouping the first, second and further sub-sets of oligonucleotides according to fragment similarity such that the two or more nucleic acid fragments assembled in the same reaction compartment are non-similar,