Born-again stars offer us a unique possibility of studying the evolution of the circumstellar envelope of evolved stars in human timescales. To present, most of the observations of the circumstellar material in these stars have been limited to study the relatively hot gas and dust. In other evolved stars, the emission from rotational transitions of molecules, such as CO, is commonly used to study the cool component of their circumstellar envelopes. Thus, the detection and study of molecular gas in born-again stars would be of great importance to understand their composition and chemical evolution. In addition, the molecular emission would be an invaluable tool to explore the physical conditions, kinematics and formation of asymmetric structures in the circumstellar envelopes of these evolved stars. However, until now, all attempts to detect molecular emission from the cool material around born-again stars have failed. We searched for emission from rotational transitions of molecules in the hydrogen-deficient circumstellar envelopes of born-again stars to explore the chemical composition, kinematics, and physical parameters of the relatively cool gas. We carried out observations using the APEX and IRAM 30m telescopes to search for molecular emission toward four well studied born-again stars, V4334 Sgr, V605 Aql, A30 and A78, that are thought to represent an evolutionary sequence. We detected for the first time emission from HCN and H13CN molecules toward V4334 Sgr, and CO emission in V605 Aql. No molecular emission was detected above the noise level toward A30 and A78. The detected lines exhibit broad linewidths ≳150 km s-1, which indicates that the emission comes from gas ejected during the born-again event, rather than from the old planetary nebula. A first estimate of the H12CN/H13CN abundance ratio in the circumstellar environment of V4334 Sgr is ≈3, which is similar to the value of the 12C/13C ratio measured from other observations. We derived a rotational temperature of T rot=13±1 K, and a total column density of N HCN=1.6±0.1×1016 cm-2 for V4334 Sgr. This result sets a lower limit on the amount of hydrogen that was ejected into the wind during the born-again event of this source. For V605 Aql, we obtained a lower limit for the integrated line intensities I 12C/I 13C>4.