Context : Aims : We have studied the molecular content of the circumstellar environs of symbiotic stellar systems , in particular of the well know objects R Aqr and CH Cyg . The study of molecules in these stars will help to understand the properties of the very inner shells around the cool stellar component , from which molecular emission is expected to come . Methods : We have performed mm-wave observations with the IRAM 30m telescope of the ^ { 12 } CO J =1 - 0 and J =2 - 1 , ^ { 13 } CO J =1 - 0 and J =2 - 1 , and SiO J =5 - 4 transitions in the symbiotic stars R Aqr , CH Cyg , and HM Sge . The data were analyzed by means of a simple analytical description of the general properties of molecular emission from the inner shells around the cool star . Numerical calculations of the expected line profiles , taking into account the level population and radiative transfer under such conditions , were also performed . Results : Weak emission of ^ { 12 } CO J =1 - 0 and J =2 - 1 was detected in R Aqr and CH Cyg ; a good line profile of ^ { 12 } CO J =2 - 1 in R Aqr was obtained . The intensities and profile shapes of the detected lines are compatible with emission coming from a very small shell around the Mira-type star , with a radius comparable to or slightly smaller than the distance to the hot dwarf companion , 10 ^ { 14 } – 2 \times 10 ^ { 14 } cm . We argue that other possible explanations are improbable . This region probably shows properties similar to those characteristic of the inner shells around standard AGB stars : outwards expansion at about 5 – 25 km s ^ { -1 } , with a significant acceleration of the gas , temperatures decreasing with radius between about 1000 and 500 K , and densities \sim 10 ^ { 9 } – 3 \times 10 ^ { 8 } cm ^ { -3 } . Our model calculations are able to explain the asymmetric line shape observed in ^ { 12 } CO J =2 - 1 from R Aqr , in which the relatively weaker red part of the profile would result from selfabsorption by the outer layers ( in the presence of a velocity increase and a temperature decrease with radius ) . The mass-loss rates are somewhat larger than in standard AGB stars , as often happens for symbiotic systems . In R Aqr , we find that the total mass of the CO emitting region is \sim 2 – 3 \times 10 ^ { -5 } M _ { \odot } , corresponding to \dot { M } \sim 5 \times 10 ^ { -6 } – 10 ^ { -5 } M _ { \odot } yr ^ { -1 } , and compatible with results obtained from dust emission . Taking into account other existing data on molecular emission , we suggest that the small extent of the molecule-rich gas in symbiotic systems is mainly due to molecule photodissociation by the radiation of the hot dwarf star . Conclusions :