Abstract. We report high-sensitivity millimetre observations of several molecular species ( 13 CO, HCN, HNC, CN, HCO + and N 2 H + ) in a sample of compact planetary nebulae. Some species such as HCO + and CN are particularly abundant compared to envelopes around AGB stars or even interstellar clouds. We have estimated the following average values for the column densities ratios: CN/HCN ∼ 2.6, HCO + /HCN ∼ 0.5, and HNC/HCN ∼ 0.4. Thus, the chemical composition of the molecular envelopes in these compact PNe appears somewhat intermediate between the composition of proto-PNe (such as CRL 2688 or CRL 618) and well evolved PNe (such as the Ring, M4-9, or the Helix). From observations of the CO isotopomers, we have estimated that the 12 C/ 13 C ratio is in the range 10 < ∼ 12 C/ 13 C < ∼ 40. These values are below those expected from standard asymptotic giant branch models and suggest non-standard mixing processes. The observed molecular abundances are compared to very recent modelling work, and we conclude that the observations are well explained, in general terms, by time-dependent gas-phase chemical models in which the ionization rate is enhanced by several orders of magnitude with respect to the average interstellar value. Thus, our observations confirm that the chemistry in the neutral shells of PNe is essentially governed by the high energy radiation from the hot central stars. The complexity of the chemical processes is increased by numerous factors linked to the properties of the central star and the geometry and degree of clumpiness of the envelope. Several aspects of the PN chemistry that remains to be understood are discussed within the frame of the available chemical models.